Use of MIRIAM Guidelines and MIRIAM Resources
The information on this page is being continually updated. If you have any information you wish to contribute, feel free to contact us!
Table of contents
- General MIRIAM Information
- MIRIAM URN syntax
- Tools using MIRIAM Registry or MIRIAM Guidelines
- File formats and Databases that use MIRIAM URNs
- Large Scale modelling efforts using MIRIAM
- Contact us
General MIRIAM information
- MIRIAM is an effort to establish the essential, minimal set of information that is sufficient to annotate a model in such a way as to enable its reuse. The requirements to achieve MIRIAM Guidelines compliance are available on the MIRIAM Guidelines page. This standard also describes the syntax by which annotations should be encoded: MIRIAM URIs. A brief summary of the syntax is provided below, while more information can be found here.
- MIRIAM Registry are composed of a database and associated services to provide support for generating and interpreting MIRIAM URIs.
The manner in which MIRIAM is used within the modelling, and other, communities can be described in numerous ways, and are listed below in order of increasing 'complexity':
- the use of the MIRIAM Guidelines to achieve annotational compliance for reusability (modelling standards)
- the ability of a tool to simply transfer, in unadulterated and uninterpreted fashion, a MIRIAM URN from one document to another (format support by tools)
- the ability of a tool to read, write or modify a MIRIAM URI (annotation editing support by tools)
- the ability to interpret, through resolution, a MIRIAM URN, for example to display a hyperlink for the URN (integration of tools with MIRIAM Registry)
- the ability to perform complex queries or aggregations of data based upon URNs, or to the resolved locations of a URN (higher level integration with MIRIAM Registry, combined with analytical strategies)
MIRIAM URN syntax
A detailed explanation of the construction of a MIRIAM URN can be found here Briefly, a MIRIAM URN is composed of a) a statement of the naming convention in use, b) a definition of the data type, and c) the identifier which specifies an entity within this data type. For example,
urn:miriam:pubmed:123456 is composed of:
urn:miriamdefines the syntax to be a URN using the MIRIAM scheme and syntax
urn:miriam:pubmedadditionally defines the data type as being 'PubMed'
urn:miriam:pubmed:123456identifies the publication having the PMID '123456' within the 'PubMed' data type
Tools using MIRIAM Registry or MIRIAM Guidelines
Arcadia is a visualisation tool for metabolic pathways. It is able to read SBML files, and generate from them an SBGN diagram, using semantic information encoded in the SBML file. SBO provides information essential to determine the appropriate SBGN glyph to incorporate in the visualisation, and these may be provided as 'sboTerm' or as MIRIAM URN annotations. Work is currently in progress to link MIRIAM URNs displayed in SBGN diagrams to online resources. In the future, MIRIAM annotations may also be used to make decisions on appropriate glyph selection where SBO terms are not available.
BioUML is an open source intergrated framework for systems biology. It consists of a workbench component which adopts a visual modeling approach, able to represent pathways encoded as SBML, CellML, or BioPAX. Editable pathway graphs are integrated with many databases, including SBO.
BioModels Database is a database of curated quantitative models in Biology that have been described in peer-reviewed publications. Models are annotated and cross-referenced with relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. Models deposited in the curated branch of the database comply with the MIRIAM Guidelines, and contain annotations using the MIRIAM syntax. Each of these annotations may be resolved to a URL using MIRIAM Registry, allowing the display of clickable links.
BridgeDb is a software framework that provides gene, protein and metabolite identifier mapping services. BridgeDb relies upon MIRIAM URNs as globally unique identifiers.
CellDesigner is a visual editor of gene-regulatory and biochemical networks, which also links directly to various resource databases such as PubMed. Networks are depicted in SBGN, and stored as SBML files. CellDesigner provides an option to save files containing SBO annotations. CellDesigner version 4.1 allows the creation of MIRIAM annotations, as well as a means to resolve them to retrieve information from referenced URLs.
COPASI is a tool for the simulation and analysis of biochemical networks. It supports models in the SBML format. COPASI allows the incorporation of MIRIAM style annotations into model files, storing both the reference to the external resource, and the relationship of that reference to the model component, using MIRIAM qualifiers. COPASI is not currently able to export MIRIAM annotations to SBML files, though a solution is being sought. More information on supported MIRIAM annotations can be found here. In addition, MIRIAM Registry is used to update the list of available data types, prior to the creation of any new annotations. More detailed information on this process can be found here. Information on the COPASI file format can be found here.
cPath is a web application for collecting, storing, and querying biological pathway data, which can be exported to third-party software, such as Cytoscape, for visualization and analysis. Recent publication suggests integration of the resources listed in MIRIAM Registry to facilitate data integration.
European Membrane Protein Consortium
The European Membrane Protein Consortium (E-MeP) is a European initiative devoted to the structural biology of integral membrane proteins. The E-MeP Consortium focuses particularly on membrane protein production, purification, and crystallisation; X-ray crystallography and structure determination; technology development, with a focus on high-throughput methods. For their internal perennial identification needs, the consortium used MIRIAM URIs, as well as the resolving system of MIRIAM Registry.
GetBonNie is a web-based application for building, analyzing, and sharing rule-based models encoded in the BioNetGen language (BNGL). It is designed to encourage compliance with the MIRIAM Guidelines.
libSBML is a free, open-source application programming interface to read, write, manipulate, translate, and validate SBML files. It is written in ISO C and C++ but can be used from most commonly used programing languages. While libSBML provides the basic facilities for reading and writing MIRIAM annotations from and to models, it is beyond the scope of libSBML to provide interpretation of these terms. This function is provided by other libraries.
libAnnotationSBML is a java library which has been developed for the specific purpose of exploiting SBML annotations. The libAnnotationSBML library acts as a layer on top of libSBML, linking SBML annotations to the web services that describe the annotated terms. The links between MIRIAM-compliant annotations in the SBML files and the physical locations that are referenced for each annotation is built by querying MIRIAM Registry, thereby retrieving the details of each of these data types including names, URNs and physical URLs linking to specific resources.
MEMOSys, the web based Metabolic Model System (MEMOSys) is a platform for the management, storage, and development of metabolic models. It incorporates a versioning system, providing a complete reconstruction history, and a search system. Models contain references to external databases, stored using MIRIAM URNs, and are presented to the user as hyperlinks.
PathText is a system designed to integrate pathway visualisation, text mining and annotation tools. It handles SBML files, and can use MIRIAM URNs to generate specific queries to assist in text mining of information.
The next version of Pathway Commons (currently under development) is using MIRIAM URNs for their identifier needs.
Pathway Editor is a program that allows pathway creation and download fof existing pathways from selected sources such as KEGG. It uses an SBML plugin, allowing the ability to read and edit MIRIAM URNs.
Payao is a collaborative web-based platform to enable community-level sharing, annotation and curation of models. It reads SBML files, displays them using CellDesigner (SBGN compliant), and will allow addition of MIRIAM URNs as tags within representations.
SABIO-RK: System for the Analysis of Biochemical Pathways - Reaction Kinetics (SABIO-RK) is a web-accessible curated database offering information about biochemical reactions and their kinetic properties. Data about biochemical reactions and their kinetic parameters (with their respective rate equations) can be exported in SBML, allowing its import into simulation and modelling programs supporting SBML.
SAINT (SBML Annotation Integration Interface) is an interactive web tool to annotate models with MIRIAM URNs. SAINT accepts SBML-formatted files and integrates information from multiple databases automatically, using a query translation service, and presents the user with potential new annotations which can be incorporated into a model.
SBML is one of a number of formats in which models can be encoded. Others include CellML and BioPAX. There are a variety of converters available to inter-convert between SBML and other encoding formats, all of which are available here. On the most basic level, the converters are all able to read MIRIAM annotations from SBML files, and reencode them to the desired format. Some converters, for example SBML to BioPaX, additionally use the annotations to query MIRIAM Registry web services, to assist in more precise representation in the target format. The converters that generate graphical representations, for example SBML to SVG, also make use of MIRIAM Registry to generate SBGN diagrams.
SBMLeditor is a low-level editing tool to facilitate the creation and editing of SBML format files. The editor, written in Java, is capable of parsing controlled annotations in this format, and validates them against the specification. In addition, the editor allows new annotations to be entered through a user dialogue.
SBML2LaTeX is a tool to convert SBML files into a human-readable report. This report can be generated in a variety of formats, including PDF and LaTeX. This tool is available as a stand-alone java program, which requires libSBML 3.2 or higher, or online through a Graphical User Interface. Using this tool, MIRIAM URNs with a model file are converted into hyperlinked URLs in the human-readable documents generated, allowing manual confirmation of annotations within model files. The conversion of URNs to resolvable URLs is accomplished through MIRIAM Registry.
Systems Biology Metabolic Modeling assistant (SBMM) is a web application to retrieve basic metabolic information through queries, to build metabolic models, to annotate them in SBML files with MIRIAM URNs, and to generate SBGN compliant visualisations.
SemanticSBML is a tool designed to facilitate the creation and editing of SBML model annotations, and to further leverage on those annotations to enable model merging. The editor displays the SBML model file as a tree, where the node annotations are editable with MIRIAM URNs and SBO terms. Annotations can also be automatically added by the tool, based on string matching between SBML file and database files. MIRIAM annotations provide a convergence point through which models can be merged, following the resolution of identified conflicts. The tool is written in python, and runs on Linux and Windows systems. An online version is also available.
Snazer, the Simulation and Networks Analyzer, is a software prototype written in Java. It is designed to aid in the visualisation, manipulation and statistical analysis of reaction networks, thereby allowing biological models and their simulation results to be managed together and shared. Snazer is able to import SBML models, and exports to a propriety XML format, as well as to GraphML. Information embedded in the graph nodes as MIRIAM annotations is presented in the user interface.
Systems Biology Workbench
The Systems Biology Workbench (SBW) is an open source software framework that allows heterologous applications, written is diverse programming languages, to use each others capabilities via a binary-encoded message system. The system provides SBML support services based on libSBML, and includes a series of SBML translators for models implemented as 'programs', such as MATLAB. Ask Nico for more info!!.
The Virtual Cell (VCell) is a distributed application for use in computational modeling and analysis. The application, run through a web browser, requires new users to register to the system, and requires Java to use the interface. VCell is able to import and export SBML models, and permits the introduction and modification of MIRIAM-compliance annotations, as well as of MIRIAM URNs.
File formats and Databases that use MIRIAM URNs
MIRIAM URNs are used as an unambiguous, standardised and perennial identifier in a variety of formats:
- SBML: a computer-readable format for the representation of models of biological processes. SBML uses a subset of RDF, a defined syntax for the representation of metadata, combined with MIRIAM URNs to create annotation. Further information can be found here.
- SED-ML: Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. These define, for instance, the model to be used in a simualtion, parameters which need to be modified prior to a simulation, and algorithms to be used. MIRIAM URNs are used by SED-ML in defining the subject model of an experimental simulation.
- SBRML: Systems Biology Results Markup Language (SBRML) is a means of specifying quantitative results in the context of a systems biology models. As with SBML, it able to accomodate MIRIAM URNs for annotation.
- CellML: a standard based on the XML markup language, developed to store computer-based mathematical models. While MIRIAM Guidelines compliant annotations are already encodable within CellML, using for example Dublin Core, a system for utilising MIRIAM URNs is currently in progress.
- BioPAX: a format for the exchange and visualisation of biological pathway data. We are currently working with this community in order to standardise the perennial identification of the cross-refererences.
- PSI-MI: the Proteomics Standards Initiative's 'Molecular Interaction' format is a community standard data model for the representation and exchange of protein interaction data. We are currently working with this group in order to standardise the database names used in their controlled vocabularies.
- CopasiML: CopasiML is the native file format for COPASI, and is XML-based. It differs from SBML in that it also stores information regarding simulation instructions or plotting of results, which does not fit the SBML schema; SBML defers this type of data to SED-ML.
- B-Net: the YeastNet portal provides access to the consensus yeast metabolic network reconstruction. This highly annotated network is periodically updated through community collaboration. The model itself is made available as SBML files, annotated with MIRIAM URNs, or can be queried through the relational database B-Net. Queries generate participating reactions, which themselves may also be downloaded as MIRIAM URN annotated SBML files.
Large Scale modeling efforts using MIRIAM
Some of the large scale modeling efforts that have used the MIRIAM Guidelines, MIRIAM URIs for annotation, and MIRIAM Registry are highlighted below.
- Consensus yeast metabolic reconstruction: a community-level, collaborative effort was used to generate a yeast metabolic consensus model. This work entailed a large annotational effort, using MIRIAM URIs, and verification of correct annotation using MIRIAM Registry. The yeast metabolic reconstruction contains 1857 reactions, with 4861 model component annotations using MIRIAM URIs.
- Consensus human metabolic reconstruction: created in analogous manner to that for the yeast consensus model, this is another community-level, collaborative effort to generate a consensus model. To date, this metabolic reconstruction contains 8866 reactions, with 66968 model component annotations using MIRIAM URNs. This model is not yet published.
- Yeast molecular interaction network reconstruction: this reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network. The total number of different molecular species and their connecting interactions in this reconstruction is ~67,000, with 36265 model component annotations using MIRIAM URNs.
Please contact us if you would like to add your tool to this list, or with any inaccuracies or concerns you wish to draw to our attention.